NAME

       pfsearchV3 - search protein and DNA generalized profiles (version 3)

SYNOPSIS

       pfsearch [options] profile database

DESCRIPTION

       Build  protein  and DNA generalized profiles and use them to scan and align sequences, and
       search databases.

OPTIONS

   Profile
       --level
              [-l] : level to use for cutoff

       --mode [-m] : mode to use for normalization

   Database
       --create-index-database
              [-c] : output indices to given file

       --use-index-database
              [-i] : use indices stored in given file

   Heuristic
       --cutoff
              [-C] : heuristic cutoff value

       --dump-heuristic-scores
              [-A] : only print heuristic scores to stdout

       --dump-heuristic-sequences [-D] : dump passed heuristic sequences

   Filter
       --dump-filter-scores
              [-a] : only print filter scores to stdout

       --dump-filter-sequences
              [-d] : dump passed heuristic and filter sequences

   Optimizations
       --sse2 [-s] : enforces SSE 2 only instruction set

       --nthreads
              [-t] : max number of threads to use

       --max-heuristic-nthreads
              [-T] : max number of threads to use for heuristic phase only. (IO bounds)

       --no-affinity
              [-f] : disable CPU affinity file

       --thread-affinity
              [-M] : file containing thread mask, one row for one thread

       --no-shared-core
              [-k] : Prevent core resource sharing

       --split
              [-b] : if both SSE 2 & 4.1 are available, split half-half using linked resources

   Printing output
       --output-method
              [-o] : printing output method

              == 0 replicates the pfseach output without options (DEFAULT)

              == 1 simple output

              == 2 replicates pfsearch -lxz output

              == 3 replicates pfscan -lxz output

              == 4 tsv output (single line tab delimited)

       --output-length
              [-W] : maximum number of column for sequence output printing

   Other
       --verbose
              [-v] : verbose on stderr

       --help [-h] : output command help

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.